Research Briefing

Previous studies have suggested the presence of a ‘blood microbiome’. Here, we analysed sequencing data generated from the blood of 9,770 healthy individuals and found no evidence for a common blood microbiome in these individuals.

Colonoids derived from adult human stem cells support growth of human enterovirus. Instead of spreading through the epithelium or lysing infected cells, virus is released within intact infected cells. Infected cells are detected by force-sensing ion channels, a mechanism akin to that used for normal turnover of uninfected epithelia.

We present evidence that lignin, a recalcitrant and partially aromatic polymer found in plant cell walls, can be modified by anaerobic microorganisms. This finding overturns a long-standing paradigm that all biological processes of lignin degradation require oxygen and motivates further exploration of understudied biology to inform biotechnological innovation.

Human cytomegalovirus (HCMV) has two modes of infection: productive and latent. Tracking HCMV infection with single-cell transcriptomics revealed that infection outcome (productive or latent) is based on viral gene expression levels at early stages of infection. Moreover, intrinsic levels of interferon-stimulated genes affect viral gene expression and the outcome of infection.

Rebound virus in the cerebrospinal fluid revealed viral lineages selected for growth in T cells that were clonally amplified and often distinct from the majority of rebound viral lineages in the blood.

Cytotoxic CD8⁺ T cells reduce the average lifespan of productively infected cells during acute simian immunodeficiency virus infection (a primate model of human immunodeficiency virus infection). However, they are ineffective at preventing the establishment of a persistent reservoir of latently infected cells under long-term antiretroviral therapy.

Chemotaxis towards the interspecies quorum sensing signal autoinducer 2 (AI-2) promotes gut colonization by Escherichia coli and is linked to fructoselysine metabolism. The differential ability of E. coli strains to chemotactically respond to AI-2 further leads to niche segregation and co-existence of E. coli strains in the murine gut.

A combined quantitative and isotope-tracking proteomics approach illuminates how scarce nitrogen is allocated to protein biosynthesis by members of an ocean-surface microbial community. We identify taxon-specific substrate preferences and a distinct subset of functions — particularly infrastructure for protein production, folding and turnover — that constitute the bulk of community nitrogen demand.

This work shows that Akkermansia muciniphila and its metabolite, harmaline, upregulate the production of bile acid-coenzyme A: amino acid N-acyltransferase (BAAT) in hepatocytes. As a result of enhanced BAAT production, increased synthesis of conjugated primary bile acids suppresses the severe systemic inflammation caused by severe fever with thrombocytopenia syndrome virus infection.

Pandemic viruses cause major global disease burden and economic disruption. We investigated pandemic HIV-1(M) to understand its unique characteristics by comparing it with HIV strains that did not achieve pandemic human-to-human spread. We observed structural adaptations in the HIV-1(M) capsid that reduce detection by innate immune sensors.

Most prokaryotes cannot easily be grown in the laboratory and distributed as pure cultures. Thus, these organisms could not be officially named. A code of nomenclature — the SeqCode — provides paths to name such organisms on the basis of genomic data, aiming to unify field and laboratory studies in microbiology.

This work used DNA and RNA sequencing to investigate how wildfire burn severity affects forest soil microbiomes. The results revealed the mechanisms that allow specific bacteria, fungi and viruses to colonize and thrive in burned soils. These changes can influence nutrient cycling and carbon storage in soil.

Now, a study using multi-omics to investigate the mechanistic role of the airway microbiome in chronic obstructive pulmonary disease (COPD) reveals that the airway microbiome-derived metabolite indole-3-acetic acid (IAA) can alleviate COPD-associated airway inflammation and epithelial apoptosis. These results implicate IAA as a potential therapeutic candidate for further investigation in COPD.

Marine protists abound, but are challenging to study, and their interactions with other microbes in nature remain largely unknown. We captured wild predatory protists (choanoflagellates) and discovered a divergent, obligately co-associated bacterial group that lives by extracting resources from these predators.

The conserved nucleotide diadenosine tetraphosphate (Ap4A) is induced under various stresses, including heat. In a non-biased screen, we identified a critical role of Ap4A in inhibiting a central step in purine metabolism and heat resistance. We clarify the molecular mechanism of Ap4A action on the inosine-5′-monophosphate dehydrogenase (IMPDH) enzyme, showing Ap4A as a bona fide nucleotide second messenger.

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a phenotype that has changed fundamentally compared with preceding variants. Substantial antigenic change within the spike protein and a new endocytic entry mechanism underlie the immune evasion characteristics and a coincident decrease in the virulence of this variant.

Well-replicated, ecologically realistic, long-term field experiments were conducted to test the effects of warming on soil microbial diversity. Warming significantly reduced the biodiversity of soil bacteria, fungi and protists by altering environmental selections and biotic interactions, potentially disrupting the functional processes of the soil ecosystem.